Because according to tomreyn this kind of thread is really necessary.
Both are open source, and are thusly really easy to mod, though Pyro takes the lead here since you can export directly into opensource COLLADA format as opposed to g3d. Both engines use the really easy xml standard to define characteristics, which is tops. I haven't compared any of the xmls I've worked on with this engine with those of Pyro's; by the looks of things the only difference is there's a bit more subdivision regarding folder structure.
As far as content goes, it's really a matter of taste between Megaglest's default techtree and the ten or so available in Pyrogenesis's own flagship game, 0AD. The assets in the latter are indubitably higher quality, but there's also a bit less of them and balance is a mess at the moment. Additionally, more of an engine fault if anything is the fact that Pyro seems to be choppy on machines that should meet its system requirements, which are a bit higher than its opponent here, but should you meet them it just kicks Glest's requisite low-poly style out of the water.
So that said, is there really any reason to consider Glest as a platform for development when Pyrogenesis offers a lot more graphical flexibility? I'd like to hear thoughts on this; while a ton of people are going to obviously be very biased on this subject matter given the forum's mission, anyone's experience with Pyro compared to Glest would greatly contribute to the topic of this thread.